Handout PSM-2010

Mass Spectrometry (MS)

Mass Spectrometry (MS)

An analytical technique for measuring the mass-tocharge ratio (m/z) of ions in the gas phase mass spectrometry is our most valuable analytical tool for determining accurate molecular masses also can give information about structure proteins can now be sequenced by MS

A Mass Spectrometer
A mass spectrometer is designed to do three things
convert neutral atoms or molecules into a beam of positive (or negative) ions separate the ions on the basis of their mass-to-charge (m/z) ratio measure the relative abundance of each ion

A Mass Spectrometer
Electron Ionization MS
in the ionization chamber, the sample is bombarded with a beam of high-energy electrons collisions between these electrons and the sample result in loss of electrons from sample molecules and formation of positive ions
H H C H + eH H H C + H + 2 eH M o l e cular ion (a radical c ati on)

Molecular Ion
Molecular ion (M): a radical cation formed by removal of a single electron from a parent molecule in a mass spectrometer For our purposes, it does not matter which electron is lost; radical cation character is delocalized throughout the molecule; therefore, we write the molecular formula of the parent molecule in brackets with
a plus sign to show that it is a cation a dot to show that it has an odd number of electrons

Molecular Ion
at times, however, we find it useful to depict the radical cation at a certain position in order to better understand its reactions
CH 3 CH 2 OCH( CH 3 ) 2 . . CH 3 CH 2 OCH ( CH 3 ) 2

Mass Spectrum
Mass spectrum: a plot of the relative abundance of ions versus their mass-to-charge ratio Base peak: the most abundant peak
assigned an arbitrary intensity of 100

MS of dopamine
a partial MS of dopamine showing all peaks with intensity equal to or greater than 0.5% of base peak

The relative abundance of all other ions is reported as a % of abundance of the base peak

MS of Dopamine
the number of peaks in the MS spectrum of dopamine is given here as a function of detector sensitivity
HO HO NH 2

Other MS techniques
What we have described is called electron ionization mass spectrometry (EI-MS) Other MS techniques include
fast atom bombardment (FAB) matrix-assisted laser desorption ionization (MALDI) chemical ionization (CI) electrospray ionization (ESI)

Peak Intensity Number Relative to of Peaks Base Peak Recorded > 5% > 1% > 0.5% > 0.05% 8 31 45 120

Resolution
Resolution: a measure of how well a mass spectrometer separates ions of different mass
low resolution: refers to instruments capable of separating only ions that differ in nominal mass; that is ions that differ by at least 1 or more atomic mass units high resolution: refers to instruments capable of separating ions that differ in mass by as little as 0.0001 atomic mass unit

Resolution
C3H6O and C3H8O have nominal masses of 58 and 60, and can be distinguished by low-resolution MS C3H8O and C2H4O2 have nominal masses of 60 distinguish between them by high-resolution MS
M o l e cul ar N o m i nal Form ula M ass C3 H8 O 60 C 2 H4 O 2 60 P re c i se M as s 60.05754 60.02112

Isotopes
virtually all elements common to organic compounds are mixtures of isotopes
A to mi c El e m e nt w e i gh t Iso to pe 1 hy d ro ge n 1.0079 H 2 H 12 carbo n 12.011 13 C C 14.007 14 N ni tro ge n 15 N 15.999 1 6 O o xyg e n 18 O su l fu r 32.066 32 S 34 S 35 35.453 ch l ori ne Cl 37 Cl 79.904 79Br brom i ne 81 Br M as s Re l ativ e (am u ) A b un dan ce 1.00783 100 2.01410 0.016 12.0000 100 13.0034 1.11 14.0031 100 15.0001 0.38 15.9949 100 17.9992 0.20 31.9721 100 33.9679 4.40 34.9689 100 36.9659 32.5 78.9183 100 80.9163 98.0

Isotopes
carbon, for example, in nature is 98.90% 12C and 1.10% 113C there are 1.11 atoms of carbon-13 in nature for every 100 atoms of carbon-12
1.10 x 100 = 1.1 1 ato m s 9 8.90
13

C p e r 1 00 ato m s

12

M+2 and M+1 Peaks

The most common elements giving rise to significant M + 2 peaks are chlorine and bromine
chlorine in nature is 75.77% 35Cl and 24.23% 37Cl a ratio of M to M + 2 of approximately 3:1 indicates the presence of a single chlorine in a compound

M+2 and M+1 Peaks

bromine in nature is 50.7% 79Br and 49.3% 81Br a ratio of M to M + 2 of approximately 1:1 indicates the presence of a single bromine in a compound

M+2 and M+1 Peaks

Sulfur is the only other element common to organic compounds that gives a significant M + 2 peak

32S

Fragmentation of M
To attain high efficiency of molecular ion formation and give reproducible mass spectra, it is common to use electrons with energies of approximately 70 eV [6750 kJ (1600 kcal)/mol]
this energy is sufficient not only to dislodge one or more electrons from a molecule, but also to cause extensive fragmentation these fragments may be unstable as well and, in turn, break apart to even smaller fragments

= 95.02% and 34S = 4.21%

Because M + 1 peaks are relatively low in intensity compared to the molecular ion and often difficult to measure with any precision, they are generally not useful for accurate determinations of molecular weight

Fragmentation of M
Fragmentation of a molecular ion, M, produces a radical and a cation
only the cation is detected by MS
A -B +

Fragmentation of M
A great deal of the chemistry of ion fragmentation can be understood in terms of the formation and relative stabilities of carbocations in solution
where fragmentation occurs to form new cations, the mode that gives the most stable cation is favored the probability of fragmentation to form new carbocations increases in the order
CH 3 + < 1 < 2 3 1 al lyl i c < 2 al l yl ic < 3 al l yl ic 3 be n z y l i c 1 b e nz y l ic 2 be n z y l i c

A Rad ical + A Cation

B+ Catio n

M o le cu lar ion (a rad ical c atio n )

B R ad ical

Interpreting MS
The only elements to give significant M + 2 peaks are Cl and Br
if no large M + 2 peak is present, these elements are absent

Alkanes
Fragmentation tends to occur in the middle of unbranched chains rather than at the ends The difference in energy among allylic, benzylic, 3 , 2 1 and methyl cations is much greater than the , , difference among comparable radicals
where alternative modes of fragmentation are possible, the more stable carbocation tends to form in preference to the more stable radical

Is the mass of the molecular ion odd or even? Nitrogen Rule: if a compound has
zero or an even number of nitrogen atoms, its molecular ion will have an even m/z value an odd number of nitrogen atoms, its molecular ion will have an odd m/z value

Alkanes
MS of octane

Alkanes
MS of 2,2,4-trimethylpentane

Alkanes
MS of methylcyclopentane

Alkenes
Alkenes characteristically
show a strong molecular ion peak cleave readily to form resonance-stabilized allylic cations
+ [ CH 2 = CH CH 2 CH2 CH3 ] CH2 = CHCH2
+

CH2 CH3

Cyclohexenes
cyclohexenes give a 1,3-diene and an alkene, a process that is the reverse of a Diels-Alder reaction.
CH3
+

Alkynes
Alkynes typically
show a strong molecular ion peak cleave readily to form the resonance-stabilized propargyl cation or a substituted propargyl cation
3-P ro p y n y l catio n HC (P ro p argy l catio n) C-CH2
+

CH 3 H3 C CH 2 A ne u tral d ie ne (m /z 68) C
+

HC

C= CH 2

H3C

CH2 A radic al cation (m /z 68)

Lim on e ne (m /z 136)

Alcohols
One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18 Another common pattern is loss of an alkyl group from the carbon bearing the OH to give a resonance-stabilized oxonium ion and an alkyl radical R'
R C O H

Alcohols
MS of 1-butanol

R" M ole c ular i o n (a rad ic al catio n)

A radical

R' - C O H R'- C= O-H R" R" A re s onan ce -stab i liz e d o xo ni um i o n

Aldehydes and Ketones

Characteristic fragmentation patterns are
cleavage of a bond to the carbonyl group ( -cleavage) McLafferty rearrangement O
+ O +
- cleavage

Aldehydes and Ketones

MS of 2-octanone

m/z 43 O

m/z 128

C H3
H + McLafferty rearrangement

+ m/z 113

H +

Molecular ion m/z 114

m/z 58

Carboxylic Acids
Characteristic fragmentation patterns are
-cleavage to give the ion [CO2 McLafferty rearrangement
O OH Molecular ion m/z 88
H + OH Molecular ion m/z 88 McLafferty rearrangement

Carboxylic Acids
MS of butanoic acid H]+ of m/z 45
+

- cleavage

O = C- O - H m/z 45

H +

O OH

m/z 60

Esters
-cleavage and McLafferty rearrangement
O O C H3 Molecular ion m/z 102 + - cleavage O + m/z 71 + + O + O CH3 m/z 59 + O O CH3 m/z 74

Esters
MS of methyl butanoate
O CH3

O O CH3

McLafferty rearrangement

H +

Molecular ion m/z 102

Aromatic Hydrocarbons
most show an intense molecular ion peak most alkylbenzenes show a fragment ion of m/z 91
+

Amines
H

H - H H H H
+

The most characteristic fragmentation pattern of 1 , 2 and 3aliphatic amines is -cleavage ,

CH 3 CH 3 - CH- CH 2 - CH 2 - N H 2 - cleavage C H3 C H 3 - C H- CH 2 + + CH 2 = N H 2 m/z 30

CH 3 Toluene radical cation

H Tropylium cation (m/z 91) H